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Hi team,
Would you please suggest what cause the kernal dead error? Thank you so much! This cell ran for about 2 hours and then I got the error kernal dead.
from scenicplus.wrappers.run_pycistarget import run_pycistarget
run_pycistarget(
region_sets = region_sets,
species = 'homo_sapiens',
save_path = os.path.join(work_dir, 'motifs'),
ctx_db_path = rankings_db,
dem_db_path = scores_db,
path_to_motif_annotations = motif_annotation,
run_without_promoters = True,
n_tpu = 1,
_temp_dir = os.path.join(tmp_dir, 'ray_spill'),
annotation_version = 'v10nr_clust',
)
This is what I have in the log file:
[I 16:02:55.296 NotebookApp] Saving file at /project/multiome.ipynb
[I 16:16:57.060 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
kernel 0fc1137e-0f27-41a3-a544-4bd674cce75b restarted
[I 16:18:55.288 NotebookApp] Saving file at /project/multiome.ipynb
I found a similar issue here: #28
I run Jupyter notebook on a server.
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